BioC 2.12: CHECK report for lumi on george2

Package: lumi

Version: 2.12.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.12.0.tar.gz

StartedAt: 2013-10-09 02:58:18 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:17:27 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 1148.4 seconds

RetCode: 0

Status:  OK

CheckDir: lumi.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/lumi.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lumi’ version ‘2.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘lumi’ can be installed ... [55s/56s] OK
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    7.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
* checking Rd files ... NOTE
prepare_Rd: getChrInfo.Rd:23-25: Dropping empty section \details
prepare_Rd: getChrInfo.Rd:29-31: Dropping empty section \references
prepare_Rd: getChrInfo.Rd:38-40: Dropping empty section \seealso
prepare_Rd: getChrInfo.Rd:41-44: Dropping empty section \examples
prepare_Rd: importMethyIDAT.Rd:44-47: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [10m/10m] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
lumiMethyStatus       266.253  0.040 268.321
getNuIDMappingInfo     47.995  0.060  48.586
nuID2RefSeqID          39.779  0.016  40.061
nuID2EntrezID          37.950  0.024  38.304
plotGammaFit           18.285  0.000  18.295
methylationCall        17.465  0.016  17.485
getChipInfo            16.965  0.300  17.602
gammaFitEM             16.261  0.000  16.382
probeID2nuID           12.161  0.040  12.348
nuID2IlluminaID        11.225  0.028  11.493
nuID2targetID          11.229  0.008  11.402
nuID2probeID           11.160  0.012  11.245
targetID2nuID          10.676  0.012  10.693
MAplot-methods          8.597  0.084   8.724
adjColorBias.quantile   6.160  0.072   6.263
LumiBatch-class         5.536  0.100   5.667
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/lumi.Rcheck/00check.log’
for details.

* installing *source* package ‘lumi’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘image’ when loading ‘graphics’
Warning: replacing previous import ‘nleqslv’ when loading ‘nleqslv’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘image’ when loading ‘graphics’
Warning: replacing previous import ‘nleqslv’ when loading ‘nleqslv’
Warning: ignoring .First.lib() for package ‘lumi’
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	5.536	0.100	5.667
MAplot-methods	8.597	0.084	8.724
addAnnotationInfo	0.976	0.008	0.996
addControlData2lumi	0.012	0.004	0.015
addNuID2lumi	0.016	0.004	0.019
adjColorBias.quantile	6.160	0.072	6.263
adjColorBias.ssn	2.244	0.008	2.260
bgAdjust	0.124	0.008	0.132
bgAdjustMethylation	0.484	0.000	0.485
boxplot-MethyLumiM-methods	1.004	0.000	1.005
boxplot-methods	0.340	0.004	0.341
boxplotColorBias	2.904	0.008	2.914
density-methods	0.152	0.008	0.163
detectOutlier	0.188	0.008	0.195
detectionCall	0.232	0.020	0.255
estimateBeta	1.260	0.012	1.271
estimateIntensity	0.432	0.004	0.438
estimateLumiCV	0.152	0.008	0.158
estimateM	0.984	0.004	0.990
estimateMethylationBG	1.436	0.004	1.441
example.lumi	0.128	0.004	0.131
example.lumiMethy	0.088	0.004	0.095
example.methyTitration	0.216	0.008	0.224
gammaFitEM	16.261	0.000	16.382
getChipInfo	16.965	0.300	17.602
getControlData	1.573	0.068	1.640
getControlProbe	0.280	0.016	0.295
getControlType	0.284	0.000	0.283
getNuIDMappingInfo	47.995	0.060	48.586
hist-methods	0.144	0.012	0.156
id2seq	0.008	0.000	0.008
inverseVST	1.460	0.012	1.476
is.nuID	0.088	0.000	0.085
lumiB	0.204	0.004	0.208
lumiExpresso	1.552	0.004	1.579
lumiMethyB	0.072	0.000	0.072
lumiMethyC	2.828	0.004	2.834
lumiMethyN	0.140	0.004	0.143
lumiMethyStatus	266.253	0.040	268.321
lumiN	1.112	0.008	1.158
lumiQ	0.468	0.008	0.474
lumiR	0.028	0.000	0.030
lumiR.batch	0.008	0.000	0.005
lumiT	0.724	0.036	0.760
methylationCall	17.465	0.016	17.485
normalizeMethylation.quantile	0.404	0.008	0.411
normalizeMethylation.ssn	0.472	0.008	0.477
nuID2EntrezID	37.950	0.024	38.304
nuID2IlluminaID	11.225	0.028	11.493
nuID2RefSeqID	39.779	0.016	40.061
nuID2probeID	11.160	0.012	11.245
nuID2targetID	11.229	0.008	11.402
pairs-methods	2.520	0.028	2.771
plot-methods	4.676	0.028	4.708
plotCDF	0.244	0.008	0.253
plotColorBias1D	0.412	0.012	0.433
plotColorBias2D	0.288	0.008	0.299
plotControlData	0.349	0.004	0.349
plotDensity	0.164	0.000	0.162
plotGammaFit	18.285	0.000	18.295
plotHousekeepingGene	0.312	0.004	0.318
plotSampleRelation	1.404	0.008	1.421
plotStringencyGene	0.284	0.004	0.289
plotVST	0.740	0.036	0.779
probeID2nuID	12.161	0.040	12.348
produceGEOPlatformFile	0.268	0.000	0.268
produceGEOSubmissionFile	0.008	0.000	0.008
produceMethylationGEOSubmissionFile	0.008	0.000	0.009
seq2id	0.008	0.000	0.011
targetID2nuID	10.676	0.012	10.693
vst	2.312	0.012	2.326